Abstract: The primary cilium is a micron-scale signaling machine that projects from most cells in our bodies and is required for the detection and processing of optical, chemical and mechanical signals. Birth defects, obesity, mental retardation, and cystic organs are just a subset of the disease phenotypes seen in patients with damaged cilia. While an extensive parts list for cilia consisting of hundreds of proteins has been compiled over the last decade, a major challenge going forward is to understand how these proteins work together to allow the self-assembly and function of this remarkable structure. This proposal is based on the idea that major advances in our understanding of primary cilia will result from a systematic effort to reconstitute the assembly and function of this organelle in vitro using cell-free extracts. This biochemical analysis will draw on quantitative genetic interaction analysis of cilia proteins implicated in human diseases. I present a blueprint for this approach, integrating traditional protein biochemistry, modern imaging, and combinatorial RNAi, to understanding how centrosomes, membranes, and soluble factors cooperate to form functional cilia. This reconstitution will allow a high-resolution analysis of proteins encoded by cilia disease genes and, ultimately, the development of biochemical strategies to repair and even re-engineer ciliary function. Public Health Relevance: Most cells in our bodies communicate with the environment through an antenna-like structure called the primary cilium. Damage to cilia can cause a variety of diseases in humans, including birth defects, obesity, mental retardation, blindness, and kidney abnormalities. By understanding how signals are processed in this important cellular communication center, we hope to understand cilia-related diseases and develop new strategies to repair cilia function.